Crystallographic comparison of manganese- and iron-dependent homoprotocatechuate 2,3-dioxygenases

Protein3D: Enabling analysis and extraction of metal-containing sites from the Protein Data Bank with molSimplify

Metalloenzymes catalyze a wide range of chemical transformations, with the active site residues playing a key role in modulating chemical reactivity and selectivity. Unlike smaller synthetic catalysts, a metalloenzyme active site is embedded in a larger protein, which makes interrogation of electronic properties and geometric features with quantum mechanical calculations challenging. Here we implement the ability to fetch crystallographic structures from the Protein Data Bank and analyze the metal binding sites in the program molSimplify. We show the usefulness of the newly created protein3D class to extract the local environment around non-heme iron enzymes containing a two histidine motif and prepare 372 structures for quantum mechanical calculations. Our implementation of protein3D serves to expand the range of systems molSimplify can be used to analyze and will enable high-throughput study of metal-containing active sites in proteins.

Synthetic Advances for Mechanistic Insights: Metal-Oxygen Intermediates with a Macrocyclic Pyridinophane System

ConspectusMetalloenzymes, which are proteins containing earth-abundant transition-metal ions as cofactors in the active site, generate various metal-oxygen intermediates via activating a dioxygen molecule (O2) to mediate vital metabolic functions, such as the oxidative metabolism of xenobiotics and the biotransformation of naturally occurring molecules. By replicating the active sites of metalloenzymes, many bioinorganic chemists have studied the geometric and electronic properties and reactivities of model complexes to understand the nature of enzymatic intermediates and develop bioinspired metal catalysts. Among the reported model complexes, nonporphyrinic macrocyclic ligands are the predominant coordination system widely used in stabilizing and isolating diverse metal-oxygen intermediates, which allows us to extensively investigate the physicochemical characteristics of the analogs of reactive intermediates of metalloenzymes. In particular, it has been reported that the ring size of the macrocyclic ligands, defined by the number of atoms in the macrocyclic ring, drastically affects the identity of the metal-oxygen intermediate. Thus, systematic modification of the macrocyclic ligands has been a great subject being examined in various inorganic fields.In this Account, we describe synthetic advances of a macrocyclic ligand system by introducing pyridine donors into a 12-membered tetraazamacrocyclic ligand (12-TMC) that initially has 4 amine donors. Interestingly, the backbone of the pyridinophane ligand with 2 pyridine and 2 amine donors in a 12-membered ring is shown to be much more folded than in other macrocyclic ligands, thereby allowing the axial and equatorial donors to separately control the electronic structure of metal complexes. Then, we looked over independent electronic and steric effects on metal-oxygen species with thorough physicochemical analysis. The NiIII-peroxo complexes exhibit nucleophilic reactivity dependent on the steric hindrance of the second coordination sphere. Furthermore, the C-H bond strength of the second coordination sphere has also been an important factor in determining the stability of MnIV-bis(hydroxo) intermediates. Electronic tuning on CoIII-hydroperoxo intermediates results in a trend between the electron-donating abilities of para-substituents on pyridine in the pyridinophane ligand and electrophilic reactivities, from which mechanistic insights into the metal-hydroperoxo species have been gained. Importantly, the metal-oxygen intermediates supported by the pyridinophane ligand system have revealed quite challenging chemical reactions, including dioxygenase-like nitrile activation by CoIII-peroxo intermediates and the oxidation of aldehyde and aromatic compounds by manganese-oxygen intermediates. Based on the fine substitution of donors, we have addressed that those novel reactions originated from the unique framework of the pyridinophane system incorporating spin-crossover behavior and high redox potentials of the metal-oxygen intermediates. These results will be valuable for the structure-activity relationship of metal-oxygen intermediates, giving a better understanding on the enzymatic coordination system where amino acid ligands vary for specific chemical reactions.

Structure and biochemical characterization of an extradiol 3,4-dihydroxyphenylacetate 2,3-dioxygenase from Acinetobacter baumannii

3,4-Dihydroxyphenylacetate (DHPA) 2,3-dioxygenase (EC 1.13.11.15) from Acinetobacter baumannii (AbDHPAO) is an enzyme that catalyzes the 2,3-extradiol ring-cleavage of DHPA in the p-hydroxyphenylacetate (HPA) degradation pathway. While the biochemical reactions of various DHPAOs have been reported, only structures of DHPAO from Brevibacterium fuscum and their homologs are available. Here, we report the X-ray structure and biochemical characterization of an Fe2+-specific AbDHPAO that shares 12% sequence identity to the enzyme from B. fuscum. The 1.8 Å X-ray structure of apo-AbDHPAO was determined with four subunits per asymmetric unit, consistent with a homotetrameric structure. Interestingly, the αβ-sandwiched fold of the AbDHPAO subunit is different from the dual β-barrel-like motif of the well-characterized B. fuscum DHPAO structures; instead, it is similar to the structures of non-DHPA extradiol dioxygenases from Comamonas sp. and Sphingomonas paucimobilis. Similarly, these extradiol dioxygenases share the same chemistry owing to a conserved 2-His-1-carboxylate catalytic motif. Structure analysis and molecular docking suggested that the Fe2+ cofactor and substrate binding sites consist of the conserved residues His12, His57, and Glu238 forming a 2-His-1-carboxylate motif ligating to Fe2+ and DHPA bound with Fe2+ in an octahedral coordination. In addition to DHPA, AbDHPAO can also use other 3,4-dihydroxyphenylacetate derivatives with different aliphatic carboxylic acid substituents as substrates, albeit with low reactivity. Altogether, this report provides a better understanding of the structure and biochemical properties of AbDHPAO and its homologs, which is advancing further modification of DHPAO in future applications.

Nuclear Resonance Vibrational Spectroscopy Definition of Peroxy Intermediates in Catechol Dioxygenases: Factors that Determine Extra- versus Intradiol Cleavage

The extradiol dioxygenases (EDOs) and intradiol dioxygenases (IDOs) are nonheme iron enzymes that catalyze the oxidative aromatic ring cleavage of catechol substrates, playing an essential role in the carbon cycle. The EDOs and IDOs utilize very different FeII and FeIII active sites to catalyze the regiospecificity in their catechol ring cleavage products. The factors governing this difference in cleavage have remained undefined. The EDO homoprotocatechuate 2,3-dioxygenase (HPCD) and IDO protocatechuate 3,4-dioxygenase (PCD) provide an opportunity to understand this selectivity, as key O2 intermediates have been trapped for both enzymes. Nuclear resonance vibrational spectroscopy (in conjunction with density functional theory calculations) is used to define the geometric and electronic structures of these intermediates as FeII-alkylhydroperoxo (HPCD) and FeIII-alkylperoxo (PCD) species. Critically, in both intermediates, the initial peroxo bond orientation is directed toward extradiol product formation. Reaction coordinate calculations were thus performed to evaluate both the extra- and intradiol O-O cleavage for the simple organic alkylhydroperoxo and for the FeII and FeIII metal catalyzed reactions. These results show the FeII-alkylhydroperoxo (EDO) intermediate undergoes facile extradiol O-O bond homolysis due to its extra e-, while for the FeIII-alkylperoxo (IDO) intermediate the extradiol cleavage involves a large barrier and would yield the incorrect extradiol product. This prompted our evaluation of a viable mechanism to rearrange the FeIII-alkylperoxo IDO intermediate for intradiol cleavage, revealing a key role in the rebinding of the displaced Tyr447 ligand in this rearrangement, driven by the proton delivery necessary for O-O bond cleavage.

Underlying Role of Hydrophobic Environments in Tuning Metal Elements for Efficient Enzyme Catalysis

The catalytic functions of metalloenzymes are often strongly correlated with metal elements in the active sites. However, dioxygen-activating nonheme quercetin dioxygenases (QueD) are found with various first-row transition-metal ions when metal swapping inactivates their innate catalytic activity. To unveil the molecular basis of this seemingly promiscuous yet metal-specific enzyme, we transformed manganese-dependent QueD into a nickel-dependent enzyme by sequence- and structure-based directed evolution. Although the net effect of acquired mutations was primarily to rearrange hydrophobic residues in the active site pocket, biochemical, kinetic, X-ray crystallographic, spectroscopic, and computational studies suggest that these modifications in the secondary coordination spheres can adjust the electronic structure of the enzyme-substrate complex to counteract the effects induced by the metal substitution. These results explicitly demonstrate that such noncovalent interactions encrypt metal specificity in a finely modulated manner, revealing the underestimated chemical power of the hydrophobic sequence network in enzyme catalysis.

Charge Maintenance during Catalysis in Nonheme Iron Oxygenases

Here, the choice of the first coordination shell of the metal center is analyzed from the perspective of charge maintenance in a binary enzyme-substrate complex and an O₂-bound ternary complex in the nonheme iron oxygenases. Comparing homogentisate 1,2-dioxygenase and gentisate dioxygenase highlights the significance of charge maintenance after substrate binding as an important factor that drives the reaction coordinate. We then extend the charge analysis to several common types of nonheme iron oxygenases containing either a 2-His-1-carboxylate facial triad or a 3-His or 4-His ligand motif, including extradiol and intradiol ring-cleavage dioxygenases, thiol dioxygenases, α-ketoglutarate-dependent oxygenases, and carotenoid cleavage oxygenases. After forming the productive enzyme-substrate complex, the overall charge of the iron complex at the 0, +1, or +2 state is maintained in the remaining catalytic steps. Hence, maintaining a constant charge is crucial to promote the reaction of the iron center beginning from the formation of the Michaelis or ternary complex. The charge compensation to the iron ion is tuned not only by protein-derived carboxylate ligands but also by substrates. Overall, these analyses indicate that charge maintenance at the iron center is significant when all the necessary components form a productive complex. This charge maintenance concept may apply to most oxygen-activating metalloenzymes systems that do not draw electrons and protons step-by-step from a separate reactant, such as NADH, via a reductase. The charge maintenance perception may also be useful in proposing catalytic pathways or designing prototypical reactions using artificial or engineered enzymes for biotechnological applications.

OPFRs in e-waste sites: Integrating in silico approaches, selective bioremediation, and health risk management of residents surrounding

A multilevel index system of organophosphate flame retardant bioremediation effect in an e-waste handling area was established under three bioremediation scenarios (scenario I, plant absorption; scenario II, plant-microbial combined remediation; scenario III, microbial degradation). Directional modification of OPFR substitutes with high selective bioremediation was performed. The virtual amino acid mutation approach was utilised to generate high-efficiency selective absorption/degradation mutant proteins (MPs) in a plant-microbial system under varying conditions. In scenario III, the MP's microbial degrading ability to replace molecules was increased to the greatest degree (165.82%). Appropriate foods such as corn, pig liver, and yam should be consumed, whereas the simultaneous consumption of high protein foods such as pig liver and walnut should be avoided; sweet potato and yam are believed to be prevent OPFRs and substitute molecules from entering the human body through multiple pathways for reduced genotoxicity of OPFRs in the populations of e-waste handling areas (the reduction degree can reach 85.12%). The study provides a theoretical basis for the development of ecologically acceptable OPFR substitutes and innovative high-efficiency bioremediation MPs, as well as for the reduction of the joint toxicity risk of multiple ingestion route exposure/gene damage of OPFRs in high OPFR exposure sites.

A new thermophilic extradiol dioxygenase promises biodegradation of catecholic pollutants

Extradiol dioxygenases (EDOs) catalyze the meta cleavage of catechol into 2-hydroxymuconaldehyde, a critical step in the degradation of aromatic compounds in the environment. In the present work, a novel thermophilic extradiol dioxygenase from Thermomonospora curvata DSM43183 was cloned, expressed, and characterized by phylogenetic and biochemical analyses. This enzyme exhibited excellent thermo-tolerance, displaying optimal activity at 50 °C, remaining >40% activity at 70 °C. Structural modeling and molecular docking demonstrated that both active center and pocket-construction loops locate at the C-terminal domain. Site-specific mutants D285A, H205V, F301V based on a rational design were obtained to widen the entrance of substrates; resulting in significantly improved catalytic performance for all the 3 mutants. Compared to the wild-type, the mutant D285A showed remarkably improved activities with respect to the 3,4-dihydroxyphenylacetic acid, catechol, and 3-chlorocatechol, by 17.7, 6.9, and 3.7-fold, respectively. The results thus verified the effectiveness of modeling guided design; and confirmed that the C-terminal loop structure indeed plays a decisive role in determining catalytic ring-opening efficiency and substrate specificity of the enzyme. This study provided a novel thermostable dioxygenase with a broad substrate promiscuity for detoxifying environmental pollutants and provided a new thinking for further enzyme engineering of EDOs.

A novel Bacillus ligniniphilus catechol 2,3-dioxygenase shows unique substrate preference and metal requirement

Identification of novel enzymes from lignin degrading microorganisms will help to develop biotechnologies for biomass valorization and aromatic hydrocarbons degradation. Bacillus ligniniphilus L1 grows with alkaline lignin as the single carbon source and is a great candidate for ligninolytic enzyme identification. The first dioxygenase from strain L1 was heterologously expressed, purified, and characterized with an optimal temperature and pH of 32.5 °C and 7.4, respectively. It showed the highest activity with 3-ethylcatechol and significant activities with other substrates in the decreasing order of 3-ethylcatechol > 3-methylcatechol > 3-isopropyl catechol > 2, 3-dihydroxybiphenyl > 4-methylcatechol > catechol. It did not show activities against other tested substrates with similar structures. Most reported catechol 2,3-dioxygenases (C23Os) are Fe²⁺-dependent whereas Bacillus ligniniphilus catechol 2,3-dioxygenase (BLC23O) is more Mn²⁺- dependent. At 1 mM, Mn²⁺ led to 230-fold activity increase and Fe²⁺ led to 22-fold increase. Sequence comparison and phylogenetic analyses suggested that BL23O is different from other Mn-dependent enzymes and uniquely grouped with an uncharacterized vicinal oxygen chelate (VOC) family protein from Paenibacillus apiaries. Gel filtration analysis showed that BLC23O is a monomer under native condition. This is the first report of a C23O from Bacillus ligniniphilus L1 with unique substrate preference, metal-dependency, and monomeric structure.

Thermally stable manganese(III) peroxido complexes with hindered N3 tripodal ligands: Structures and their physicochemical properties

Mononuclear manganese(III) peroxido complexes are candidates for the reaction intermediates in manganese containing proteins, such as manganese superoxide dismutase (Mn-SOD) etc. In this study, manganese(III) peroxido complexes [Mn(O₂)(L3)] and [Mn(O₂)(L10)] ligated by anionic N3 type ligands with sterically hindered substituents, hydrotris(3-tertiary butyl-5-isopropyl-1-pyrazolyl)borate (L3^-) and hydrotris(3-adamantyl-5-isopropyl-1-pyrazolyl)borate (L10^-), respectively, were structurally characterized. These complexes are the first examples of structurally characterized five-coordinate manganese(III) peroxido complexes. Their characteristic ν(OO) and ν(MnO) stretchings were determined by using H₂¹⁸O₂ for the first time. Theoretical calculations were performed to obtain further insight into their structural parameters. The decomposed products were obtained as [{Mn^III(μ-O)(L3)}₂Mn^IV] and [Mn^III(OH){L10(O)}] from [Mn(O₂)(L3)] and [Mn(O₂)(L10)], respectively.

Shape-function of a novel metapyrocatechase, RW4-MPC: Metagenomics to SAXS data based insight into deciphering regulators of function

The oxygenases have attracted considerable attention in enzyme-mediated bioremediation of xenobiotic compounds due to their high specificity, cost-effectiveness, and targeted field applications. Here, we performed a functional metagenomics approach to cope with cultivability limitations to isolate a novel extradiol dioxygenase. Fosmid clone harboring dioxygenase gene was sequenced and analyzed by bioinformatics tools. One ring-cleaving dioxygenase RW4-MPC (metapyrocatechase) was purified and characterized to examine its degradation efficiency. The RW4-MPC was significantly active in the temperature and pH range of 5 to 40 °C, and 7-10, respectively, with an optimum temperature of 25 °C and pH 8. To gain insight into observed differential activity, Small-Angle X-ray Scattering (SAXS) data of the protein samples were analyzed, which brought forth that the RW4-MPC molecules form tight globular tetramers in solution. This native association was stable till 35 °C, and protein started to associate at higher temperatures, explaining heat-induced loss of function. Similarly, RW4-MPC aggregated or lost globular profile below pH 7 or at pH 10, respectively. The kinetic parameters showed the six folds high catalytic efficiency of RW4-MPC towards 2,3-dihydroxy biphenyl than catechol and its derivatives. RW4-MPC molecules showed remarkable retention of functionality in hypersaline conditions with more than 70% activity in a buffer having 3 M NaCl concentration. In concordance, SAXS data analysis showed retention of functional shape profile in hypersaline conditions. The halotolerant and oxygen insensitive nature of this enzyme makes it a potential candidate for bioremediation.

Crystal Structures of L-DOPA Dioxygenase from Streptomyces sclerotialus

Extradiol dioxygenases are essential biocatalysts for breaking down catechols. The vicinal oxygen chelate (VOC) superfamily contains a large number of extradiol dioxygenases, most of which are found as part of catabolic pathways degrading a variety of natural and human-made aromatic rings. The l-3,4-dihydroxyphenylalanine (L-DOPA) extradiol dioxygenases compose a multitude of pathways that produce various antibacterial or antitumor natural products. The structural features of these dioxygenases are anticipated to be distinct from those of other VOC extradiol dioxygenases. Herein, we identified a new L-DOPA dioxygenase from the thermophilic bacterium Streptomyces sclerotialus (SsDDO) through a sequence and genome context analysis. The activity of SsDDO was kinetically characterized with L-DOPA using an ultraviolet-visible spectrophotometer and an oxygen electrode. The optimal temperature of the assay was 55 °C, at which the K_m and k_cat of SsDDO were 110 ± 10 μM and 2.0 ± 0.1 s^-1, respectively. We determined the de novo crystal structures of SsDDO in the ligand-free form and as a substrate-bound complex, refined to 1.99 and 2.31 Å resolution, respectively. These structures reveal that SsDDO possesses a form IV arrangement of βαβββ modules, the first characterization of this assembly from among the VOC/type I extradiol dioxygenase protein family. Electron paramagnetic resonance spectra of Fe-NO adducts for the resting and substrate-bound enzyme were obtained. This work contributes to our understanding of a growing class of topologically distinct VOC dioxygenases, and the obtained structural features will improve our understanding of the extradiol cleavage reaction within the VOC superfamily.

The role of halogen substituents and substrate pKa in defining the substrate specificity of 2,6-dichlorohydroquinone 1,2-dioxygenase (PcpA)

2,6-Dichlorohydroquinone 1,2-dioxygenase (PcpA) is a non-heme Fe(II) enzyme that is specific for ortho-dihalohydroquinones. Here we deconvolute the role of halogen polarizability vs. substrate pK_a in defining this specificity, and show how substrate binding compares to the structurally homologous catechol extradiol dioxygenases. The substrates 2,6-dichloro- and 2,6-dibromohydroquinone (polarizable halogens, pK_a1 = 7.3), 2,6-difluorohydroquinone (nonpolarizable halogens, pK_a1 = 7.5), and 2-chloro-6-methylhydroquinone (polarizable halogen, pK_a1 = 9.0) were examined through spectrophotometric titrations and steady-state kinetics. The results show that binding of the substrates to the enzyme decreased [Formula: see text] by about 0.5, except for 2,6-difluorohydroquinone, which showed no change. Additionally, the K_d values of 2,6-dichloro- and 2,6-dibromohydroquinone are about equal to their respective [Formula: see text]. For comparison, with catechol 2,3-dioxygenase (XylE), the substrates 4-methyl- and 3-bromocatechol are bound to the enzyme exclusively in the monoanion form over a wide pH range, indicating a [Formula: see text] of at least - 2.9 and - 1.2, respectively. The steady-state kinetic studies showed that 2,6-difluorohydroquinone is a poor substrate, with [Formula: see text] approximately 40-fold lower and [Formula: see text] 20-fold higher than 2,6-dichlorohydroquinone, despite its similar pK_a1. Likewise, the pH dependence of [Formula: see text] for 2-chloro-6-methylhydroquinone is nearly identical to that of 2,6-dichlorohydroquinone, despite its very different pK_a1. These results show that (1) it is clearly the halogen polarizability and not the lower substrate pK_a that determines the substrate specificity of PcpA, and (2) that PcpA, unlike the catechol extradiol dioxygenases, lacks an active site base that assists with substrate deprotonation, highlighting a key functional difference in what are otherwise similar active sites that defines their different reactivity.

A Mn(iv)-peroxo complex in the reactions with proton donors

Protons play an important role in promoting O-O or M-O bond cleavage of metal-peroxo complexes. Treatment of side-on O2-bound [PPN][MnIV(TMSPS3)(O2)] (1, PPN = bis(triphenylphosphine)iminium and TMSPS3H3 = 2,2',2''-trimercapto-3,3',3''-tris(trimethylsilyl)triphenylphosphine) with perchloric acid (HClO4) in the presence of PR3 (R = phenyl or p-tolyl) results in the formation of neutral five-coordinate MnIII(OPR3)(TMSPS3) complexes (R = phenyl, 2a; p-tolyl, 2b), which are confirmed by X-ray crystallography. Isotope labelling experiments demonstrate that the oxygen atom in the phosphine oxide product derives from the peroxo ligand of 1. Reactions of 1 with weak proton donors, such as phenylthiol, phenol, substituted phenol and methanol, are also investigated to explore the reactivity of the MnIV-peroxo complex, leading to the isolation of a series of five-coordinate [MnIII(L)(TMSPS3)]- complexes (L = phenylthiolate, phenolate or methoxide). Mechanistic aspects of the reactions of the MnIV-peroxo complex with proton donors are discussed as well.

Nuclear Resonance Vibrational Spectroscopy Definition of O2 Intermediates in an Extradiol Dioxygenase: Correlation to Crystallography and Reactivity

The extradiol dioxygenases are a large subclass of mononuclear nonheme Fe enzymes that catalyze the oxidative cleavage of catechols distal to their OH groups. These enzymes are important in bioremediation, and there has been significant interest in understanding how they activate O₂. The extradiol dioxygenase homoprotocatechuate 2,3-dioxygenase (HPCD) provides an opportunity to study this process, as two O₂ intermediates have been trapped and crystallographically defined using the slow substrate 4-nitrocatechol (4NC): a side-on Fe-O₂-4NC species and a Fe-O₂-4NC peroxy bridged species. Also with 4NC, two solution intermediates have been trapped in the H200N variant, where H200 provides a second-sphere hydrogen bond in the wild-type enzyme. While the electronic structure of these solution intermediates has been defined previously as Fe^III-superoxo-catecholate and Fe^III-peroxy-semiquinone, their geometric structures are unknown. Nuclear resonance vibrational spectroscopy (NRVS) is an important tool for structural definition of nonheme Fe-O₂ intermediates, as all normal modes with Fe displacement have intensity in the NRVS spectrum. In this study, NRVS is used to define the geometric structure of the H200N-4NC solution intermediates in HPCD as an end-on Fe^III-superoxo-catecholate and an end-on Fe^III-hydroperoxo-semiquinone. Parallel calculations are performed to define the electronic structures and protonation states of the crystallographically defined wild-type HPCD-4NC intermediates, where the side-on intermediate is found to be a Fe^III-hydroperoxo-semiquinone. The assignment of this crystallographic intermediate is validated by correlation to the NRVS data through computational removal of H200. While the side-on hydroperoxo semiquinone intermediate is computationally found to be nonreactive in peroxide bridge formation, it is isoenergetic with a superoxo catecholate species that is competent in performing this reaction. This study provides insight into the relative reactivities of Fe^III-superoxo and Fe^III-hydroperoxo intermediates in nonheme Fe enzymes and into the role H200 plays in facilitating extradiol catalysis.

Biological functions controlled by manganese redox changes in mononuclear Mn-dependent enzymes

Remarkably few enzymes are known to employ a mononuclear manganese ion that undergoes changes in redox state during catalysis. Many questions remain to be answered about the role of substrate binding and/or protein environment in modulating the redox properties of enzyme-bound Mn(II), the nature of the dioxygen species involved in the catalytic mechanism, and how these enzymes acquire Mn(II) given that many other metal ions in the cell form more stable protein complexes. Here, we summarize current knowledge concerning the structure and mechanism of five mononuclear manganese-dependent enzymes: superoxide dismutase, oxalate oxidase (OxOx), oxalate decarboxylase (OxDC), homoprotocatechuate 3,4-dioxygenase, and lipoxygenase (LOX). Spectroscopic measurements and/or computational studies suggest that Mn(III)/Mn(II) are the catalytically active oxidation states of the metal, and the importance of 'second-shell' hydrogen bonding interactions with metal ligands has been demonstrated for a number of examples. The ability of these enzymes to modulate the redox properties of the Mn(III)/Mn(II) couple, thereby allowing them to generate substrate-based radicals, appears essential for accessing diverse chemistries of fundamental importance to organisms in all branches of life.

3,4-Dihydroxyphenylacetate 2,3-dioxygenase from Pseudomonas aeruginosa: An Fe(II)-containing enzyme with fast turnover

3,4-dihydroxyphenylacetate (DHPA) dioxygenase (DHPAO) from Pseudomonas aeruginosa (PaDHPAO) was overexpressed in Escherichia coli and purified to homogeneity. As the enzyme lost activity over time, a protocol to reactivate and conserve PaDHPAO activity has been developed. Addition of Fe(II), DTT and ascorbic acid or ROS scavenging enzymes (catalase or superoxide dismutase) was required to preserve enzyme stability. Metal content and activity analyses indicated that PaDHPAO uses Fe(II) as a metal cofactor. NMR analysis of the reaction product indicated that PaDHPAO catalyzes the 2,3-extradiol ring-cleavage of DHPA to form 5-carboxymethyl-2-hydroxymuconate semialdehyde (CHMS) which has a molar absorptivity of 32.23 mM^-1cm^-1 at 380 nm and pH 7.5. Steady-state kinetics under air-saturated conditions at 25°C and pH 7.5 showed a K_m for DHPA of 58 ± 8 μM and a k_cat of 64 s^-1, indicating that the turnover of PaDHPAO is relatively fast compared to other DHPAOs. The pH-rate profile of the PaDHPAO reaction shows a bell-shaped plot that exhibits a maximum activity at pH 7.5 with two pK_a values of 6.5 ± 0.1 and 8.9 ± 0.1. Study of the effect of temperature on PaDHPAO activity indicated that the enzyme activity increases as temperature increases up to 55°C. The Arrhenius plot of ln(k’_cat) versus the reciprocal of the absolute temperature shows two correlations with a transition temperature at 35°C. Two activation energy values (E_a) above and below the transition temperature were calculated as 42 and 14 kJ/mol, respectively. The data imply that the rate determining steps of the PaDHPAO reaction at temperatures above and below 35°C may be different. Sequence similarity network analysis indicated that PaDHPAO belongs to the enzyme clusters that are largely unexplored. As PaDHPAO has a high turnover number compared to most of the enzymes previously reported, understanding its biochemical and biophysical properties should be useful for future applications in biotechnology.

Oxygen activation by mononuclear nonheme iron dioxygenases involved in the degradation of aromatics

Molecular oxygen is utilized in numerous metabolic pathways fundamental for life. Mononuclear nonheme iron-dependent oxygenase enzymes are well known for their involvement in some of these pathways, activating O₂ so that oxygen atoms can be incorporated into their primary substrates. These reactions often initiate pathways that allow organisms to use stable organic molecules as sources of carbon and energy for growth. From the myriad of reactions in which these enzymes are involved, this perspective recounts the general mechanisms of aromatic dihydroxylation and oxidative ring cleavage, both of which are ubiquitous chemical reactions found in life-sustaining processes. The organic substrate provides all four electrons required for oxygen activation and insertion in the reactions mediated by extradiol and intradiol ring-cleaving catechol dioxygenases. In contrast, two of the electrons are provided by NADH in the cis-dihydroxylation mechanism of Rieske dioxygenases. The catalytic nonheme Fe center, with the aid of active site residues, facilitates these electron transfers to O₂ as key elements of the activation processes. This review discusses some general questions for the catalytic strategies of oxygen activation and insertion into aromatic compounds employed by mononuclear nonheme iron-dependent dioxygenases. These include: (1) how oxygen is activated, (2) whether there are common intermediates before oxygen transfer to the aromatic substrate, and (3) are these key intermediates unique to mononuclear nonheme iron dioxygenases?

Theoretical investigation on proton transfer mechanism of extradiol dioxygenase

The formation mechanism of alkyl(hydro)peroxo species is performed via two parallel pathways.

A bioinspired heterogeneous catalyst based on the model of the manganese-dependent dioxygenase for selective oxidation using dioxygen

A hybrid bioinspired material with manganese(ii) complexes grafted on the surface of a mesostructured porous silica is investigated.

Oxygen activation by mononuclear Mn, Co, and Ni centers in biology and synthetic complexes

The active sites of metalloenzymes that catalyze O₂-dependent reactions generally contain iron or copper ions. However, several enzymes are capable of activating O₂ at manganese or nickel centers instead, and a handful of dioxygenases exhibit activity when substituted with cobalt. This minireview summarizes the catalytic properties of oxygenases and oxidases with mononuclear Mn, Co, or Ni active sites, including oxalate-degrading oxidases, catechol dioxygenases, and quercetin dioxygenase. In addition, recent developments in the O₂ reactivity of synthetic Mn, Co, or Ni complexes are described, with an emphasis on the nature of reactive intermediates featuring superoxo-, peroxo-, or oxo-ligands. Collectively, the biochemical and synthetic studies discussed herein reveal the possibilities and limitations of O₂ activation at these three "overlooked" metals.

Enzyme Substrate Complex of the H200C Variant of Homoprotocatechuate 2,3-Dioxygenase: Mössbauer and Computational Studies

The extradiol, aromatic ring-cleaving enzyme homoprotocatechuate 2,3-dioxygenase (HPCD) catalyzes a complex chain of reactions that involve second sphere residues of the active site. The importance of the second-sphere residue His200 was demonstrated in studies of HPCD variants, such as His200Cys (H200C), which revealed significant retardations of certain steps in the catalytic process as a result of the substitution, allowing novel reaction cycle intermediates to be trapped for spectroscopic characterization. As the H200C variant largely retains the wild-type active site structure and produces the correct ring-cleaved product, this variant presents a valuable target for mechanistic HPCD studies. Here, the high-spin Fe(II) states of resting H200C and the H200C-homoprotocatechuate enzyme-substrate (ES) complex have been characterized with Mössbauer spectroscopy to assess the electronic structures of the active site in these states. The analysis reveals a high-spin Fe(II) center in a low symmetry environment that is reflected in the values of the zero-field splitting (ZFS) (D ≈ - 8 cm(-1), E/D ≈ 1/3 in ES), as well as the relative orientations of the principal axes of the (57)Fe magnetic hyperfine (A) and electric field gradient (EFG) tensors relative to the ZFS tensor axes. A spin Hamiltonian analysis of the spectra for the ES complex indicates that the magnetization axis of the integer-spin S = 2 Fe(II) system is nearly parallel to the symmetry axis, z, of the doubly occupied dxy ground orbital deduced from the EFG and A-values, an observation, which cannot be rationalized by DFT assisted crystal-field theory. In contrast, ORCA/CASSCF calculations for the ZFS tensor in combination with DFT calculations for the EFG- and A-tensors describe the experimental data remarkably well.

Unravelling the Molecular Origin of the Regiospecificity in Extradiol Catechol Dioxygenases

Many factors have been suggested to control the selectivity for extradiol or intradiol cleavage in catechol dioxygenases. The varied selectivity of model complexes and the ability to force an extradiol enzyme to do intradiol cleavage indicate that the problem may be complex. In this paper we focus on the regiospecificity of the proximal extradiol dioxygenase, homoprotocatechuate 2,3-dioxygenase (HPCD), for which considerable advances have been made in our understanding of the mechanism from an experimental and computational standpoint. Two key steps in the reaction mechanism were investigated: (1) attack of the substrate by the superoxide moiety and (2) attack of the substrate by the oxyl radical generated by O-O bond cleavage. The selectivity at both steps was investigated through a systematic study of the role of the substrate and the first and second coordination spheres. For the isolated native substrate, intradiol cleavage is calculated to be both kinetically and thermodynamically favored, therefore nature must use the enzyme environment to reverse this preference. Two second sphere residues were found to play key roles in controlling the regiospecificity of the reaction: Tyr257 and His200. Tyr257 controls the selectivity by modulating the electronic structure of the substrate, while His200 controls selectivity through steric effects and by preventing alternative pathways to intradiol cleavage.

Intrinsic Carbon-Carbon Bond Reactivity at the Manganese Center of Oxalate Decarboxylase from Density Functional Theory

The detailed manganese-dependent chemistry employed by oxalate decarboxylase (OxDC) to catalyze the nonoxidative decarboxylation of oxalic acid remains poorly understood. For example, enzyme activity requires the presence of dioxygen even though this compound is not a formal substrate in the reaction. We now report density functional theory (DFT) calculations upon a series of hypothetical OxDC active site model structures. Our results suggest that the function of the metal ion may be to position dioxygen and oxalate such that electrons can be shuttled directly between these species, thereby removing the need for the existence of Mn(III) as an intermediate in the mechanism. These calculations also indicate that the intrinsic, gas-phase reactivity of the Bacillus subtilis oxalate decarboxylase active center is to oxidize oxalate. Since this reactivity is not observed for OxDC, our DFT results suggest that protein environment modulates the intrinsic metallocenter reactivity, presumably by affecting the electronic distribution at the manganese center during catalysis.

A Long-Lived Fe(III)-(Hydroperoxo) Intermediate in the Active H200C Variant of Homoprotocatechuate 2,3-Dioxygenase: Characterization by Mössbauer, Electron Paramagnetic Resonance, and Density Functional Theory Methods

The extradiol-cleaving dioxygenase homoprotocatechuate 2,3-dioxygenase (HPCD) binds substrate homoprotocatechuate (HPCA) and O2 sequentially in adjacent ligand sites of the active site Fe(II). Kinetic and spectroscopic studies of HPCD have elucidated catalytic roles of several active site residues, including the crucial acid-base chemistry of His200. In the present study, reaction of the His200Cys (H200C) variant with native substrate HPCA resulted in a decrease in both kcat and the rate constants for the activation steps following O2 binding by >400 fold. The reaction proceeds to form the correct extradiol product. This slow reaction allowed a long-lived (t1/2 = 1.5 min) intermediate, H200C-HPCAInt1 (Int1), to be trapped. Mössbauer and parallel mode electron paramagnetic resonance (EPR) studies show that Int1 contains an S1 = 5/2 Fe(III) center coupled to an SR = 1/2 radical to give a ground state with total spin S = 2 (J > 40 cm(-1)) in Hexch = JŜ1·ŜR. Density functional theory (DFT) property calculations for structural models suggest that Int1 is a (HPCA semiquinone(•))Fe(III)(OOH) complex, in which OOH is protonated at the distal O and the substrate hydroxyls are deprotonated. By combining Mössbauer and EPR data of Int1 with DFT calculations, the orientations of the principal axes of the (57)Fe electric field gradient and the zero-field splitting tensors (D = 1.6 cm(-1), E/D = 0.05) were determined. This information was used to predict hyperfine splittings from bound (17)OOH. DFT reactivity analysis suggests that Int1 can evolve from a ferromagnetically coupled Fe(III)-superoxo precursor by an inner-sphere proton-coupled-electron-transfer process. Our spectroscopic and DFT results suggest that a ferric hydroperoxo species is capable of extradiol catalysis.

Structural Basis for Substrate and Oxygen Activation in Homoprotocatechuate 2,3-Dioxygenase: Roles of Conserved Active Site Histidine 200

Kinetic and spectroscopic studies have shown that the conserved active site residue His200 of the extradiol ring-cleaving homoprotocatechuate 2,3-dioxygenase (FeHPCD) from Brevibacterium fuscum is critical for efficient catalysis. The roles played by this residue are probed here by analysis of the steady-state kinetics, pH dependence, and X-ray crystal structures of the FeHPCD position 200 variants His200Asn, His200Gln, and His200Glu alone and in complex with three catecholic substrates (homoprotocatechuate, 4-sulfonylcatechol, and 4-nitrocatechol) possessing substituents with different inductive capacity. Structures determined at 1.35-1.75 Å resolution show that there is essentially no change in overall active site architecture or substrate binding mode for these variants when compared to the structures of the wild-type enzyme and its analogous complexes. This shows that the maximal 50-fold decrease in kcat for ring cleavage, the dramatic changes in pH dependence, and the switch from ring cleavage to ring oxidation of 4-nitrocatechol by the FeHPCD variants can be attributed specifically to the properties of the altered second-sphere residue and the substrate. The results suggest that proton transfer is necessary for catalysis, and that it occurs most efficiently when the substrate provides the proton and His200 serves as a catalyst. However, in the absence of an available substrate proton, a defined proton-transfer pathway in the protein can be utilized. Changes in the steric bulk and charge of the residue at position 200 appear to be capable of altering the rate-limiting step in catalysis and, perhaps, the nature of the reactive species.

Function of different amino acid residues in the reaction mechanism of gentisate 1,2-dioxygenases deduced from the analysis of mutants of the salicylate 1,2-dioxygenase from Pseudaminobacter salicylatoxidans

The genome of the α-proteobacterium Pseudaminobacter salicylatoxidans codes for a ferrous iron containing ring-fission dioxygenase which catalyzes the 1,2-cleavage of (substituted) salicylate(s), gentisate (2,5-dihydroxybenzoate), and 1-hydroxy-2-naphthoate. Sequence alignments suggested that the "salicylate 1,2-dioxygenase" (SDO) from this strain is homologous to gentisate 1,2-dioxygenases found in bacteria, archaea and fungi. In the present study the catalytic mechanism of the SDO and gentisate 1,2-dioxygenases in general was analyzed based on sequence alignments, mutational and previously performed crystallographic studies and mechanistic comparisons with "extradiol- dioxygenases" which cleave aromatic nuclei in the 2,3-position. Different highly conserved amino acid residues that were supposed to take part in binding and activation of the organic substrates were modified in the SDO by site-specific mutagenesis and the enzyme variants subsequently analyzed for the conversion of salicylate, gentisate and 1-hydroxy-2-naphthoate. The analysis of enzyme variants which carried exchanges in the positions Arg83, Trp104, Gly106, Gln108, Arg127, His162 and Asp174 demonstrated that Arg83 and Arg127 were indispensable for enzymatic activity. In contrast, residual activities were found for variants carrying mutations in the residues Trp104, Gly106, Gln108, His162, and Asp174 and some of these mutants still could oxidize gentisate, but lost the ability to convert salicylate. The results were used to suggest a general reaction mechanism for gentisate-1,2-dioxygenases and to assign to certain amino acid residues in the active site specific functions in the cleavage of (substituted) salicylate(s).

Geometric and electronic structure of a peroxomanganese(III) complex supported by a scorpionate ligand

A monomeric Mn(II) complex has been prepared with the facially-coordinating Tp(Ph2) ligand, (Tp(Ph2) = hydrotris(3,5-diphenylpyrazol-1-yl)borate). The X-ray crystal structure shows three coordinating solvent molecules resulting in a six-coordinate complex with Mn-ligand bond lengths that are consistent with a high-spin Mn(II) ion. Treatment of this Mn(II) complex with excess KO2 at room temperature resulted in the formation of a Mn(III)-O2 complex that is stable for several days at ambient conditions, allowing for the determination of the X-ray crystal structure of this intermediate. The electronic structure of this peroxomanganese(III) adduct was examined by using electronic absorption, electron paramagnetic resonance (EPR), low-temperature magnetic circular dichroism (MCD), and variable-temperature variable-field (VTVH) MCD spectroscopies. Density functional theory (DFT), time-dependent (TD)-DFT, and multireference ab initio CASSCF/NEVPT2 calculations were used to assign the electronic transitions and further investigate the electronic structure of the peroxomanganese(III) species. The lowest ligand-field transition in the electronic absorption spectrum of the Mn(III)-O2 complex exhibits a blue shift in energy compared to other previously characterized peroxomanganese(III) complexes that results from a large axial bond elongation, reducing the metal-ligand covalency and stabilizing the σ-antibonding Mn dz(2) MO that is the donor MO for this transition.

Molecular mechanism of strict substrate specificity of an extradiol dioxygenase, DesB, derived from Sphingobium sp. SYK-6

DesB, which is derived from Sphingobium sp. SYK-6, is a type II extradiol dioxygenase that catalyzes a ring opening reaction of gallate. While typical extradiol dioxygenases show broad substrate specificity, DesB has strict substrate specificity for gallate. The substrate specificity of DesB seems to be required for the efficient growth of S. sp. SYK-6 using lignin-derived aromatic compounds. Since direct coordination of hydroxyl groups of the substrate to the non-heme iron in the active site is a critical step for the catalytic reaction of the extradiol dioxygenases, the mechanism of the substrate recognition and coordination of DesB was analyzed by biochemical and crystallographic methods. Our study demonstrated that the direct coordination between the non-heme iron and hydroxyl groups of the substrate requires a large shift of the Fe (II) ion in the active site. Mutational analysis revealed that His124 and His192 in the active site are essential to the catalytic reaction of DesB. His124, which interacts with OH (4) of the bound gallate, seems to contribute to proper positioning of the substrate in the active site. His192, which is located close to OH (3) of the gallate, is likely to serve as the catalytic base. Glu377' interacts with OH (5) of the gallate and seems to play a critical role in the substrate specificity. Our biochemical and structural study showed the substrate recognition and catalytic mechanisms of DesB.

A two-electron-shell game: intermediates of the extradiol-cleaving catechol dioxygenases

Extradiol-cleaving catechol dioxygenases function by binding both the organic substrate and O2 at a divalent metal center in the active site. They have proven to be a particularly versatile group of enzymes with which to study the O2 activation process. Here, recent studies of homoprotocatechuate 2,3-dioxygenase are summarized, showing how nature can utilize the enzyme structure and the properties of the metal and the substrate to select among many possible chemical paths to achieve both specificity and efficiency. Possible intermediates in the mechanism have been trapped by swapping active-site metals, introducing active-site amino acid substituted variants, and using substrates with different electron-donating capacities. Although each of these intermediates could form part of a viable reaction pathway, kinetic measurements significantly limit the likely candidates. Structural, kinetic, spectroscopic, and computational analyses of the various intermediates shed light on how catalytic efficiency can be achieved.

Bioinspired manganese(ii) complexes with a clickable ligand for immobilisation on a solid support

Structural and magnetic characterization of dinuclear manganese(ii) complexes mimicking the active sites of MnD were prepared with an alkyne side function for click chemistry grafting that was tested on MCM-41 silicas.

NO binding to Mn-substituted homoprotocatechuate 2,3-dioxygenase: relationship to O₂ reactivity

Iron(II)-containing homoprotocatechuate 2,3-dioxygenase (FeHPCD) activates O2 to catalyze the aromatic ring opening of homoprotocatechuate (HPCA). The enzyme requires Fe(II) for catalysis, but Mn(II) can be substituted (MnHPCD) with essentially no change in the steady-state kinetic parameters. Near simultaneous O2 and HPCA activation has been proposed to occur through transfer of an electron or electrons from HPCA to O2 through the divalent metal. In O2 reactions with MnHPCD-HPCA and the 4-nitrocatechol (4NC) complex of the His200Asn (H200N) variant of FeHPCD, this transfer has resulted in the detection of a transient M(III)-O2 (·-) species that is not observed during turnover of the wild-type FeHPCD. The factors governing formation of the M(III)-O2 (·-) species are explored here by EPR spectroscopy using MnHPCD and nitric oxide (NO) as an O2 surrogate. Both the HPCA and the dihydroxymandelic substrate complexes of MnHPCD bind NO, thus representing the first reported stable MnNO complexes of a nonheme enzyme. In contrast, the free enzyme, the MnHPCD-4NC complex, and the MnH200N and MnH200Q variants with or without HPCA bound do not bind NO. The MnHPCD-ligand complexes that bind NO are also active in normal O2-linked turnover, whereas the others are inactive. Past studies have shown that FeHPCD and the analogous variants and catecholic ligand complexes all bind NO, and are active in normal turnover. This contrasting behavior may stem from the ability of the enzyme to maintain the approximately 0.8-V difference in the solution redox potentials of Fe(II) and Mn(II). Owing to the higher potential of Mn, the formation of the NO adduct or the O2 adduct requires both strong charge donation from the bound catecholic ligand and additional stabilization by interaction with the active-site His200. The same nonoptimal electronic and structural forces that prevent NO and O2 binding in MnHPCD variants may lead to inefficient electron transfer from the catecholic substrate to the metal center in variants of FeHPCD during O2-linked turnover. Accordingly, past studies have shown that intermediate Fe(III) species are observed for these mutant enzymes.

Spectroscopic studies of the mononuclear non-heme Fe(II) enzyme FIH: second-sphere contributions to reactivity

Factor inhibiting hypoxia-inducible factor (FIH) is an α-ketoglutarate (αKG)-dependent enzyme which catalyzes hydroxylation of residue Asn803 in the C-terminal transactivation domain (CAD) of hypoxia-inducible factor 1α (HIF-1α) and plays an important role in cellular oxygen sensing and hypoxic response. Circular dichroism (CD), magnetic circular dichroism (MCD), and variable-temperature, variable-field (VTVH) MCD spectroscopies are used to determine the geometric and electronic structures of FIH in its (Fe(II)), (Fe(II)/αKG), and (Fe(II)/αKG/CAD) forms. (Fe(II))FIH and (Fe(II)/αKG)FIH are found to be six-coordinate (6C), whereas (Fe(II)/αKG/CAD)FIH is found to be a 5C/6C mixture. Thus, FIH follows the general mechanistic strategy of non-heme Fe(II) enzymes. Modeling shows that, when Arg238 of FIH is removed, the facial triad carboxylate binds to Fe(II) in a bidentate mode with concomitant lengthening of the Fe(II)/αKG carbonyl bond, which would inhibit the O2 reaction. Correlations over α-keto acid-dependent enzymes and with the extradiol dioxygenases show that members of these families (where both the electron source and O2 bind to Fe(II)) have a second-sphere residue H-bonding to the terminal oxygen of the carboxylate, which stays monodentate. Alternatively, structures of the pterin-dependent and Rieske dioxygenases, which do not have substrate binding to Fe(II), lack H-bonds to the carboxylate and thus allow its bidentate coordination which would direct O2 reactivity. Finally, vis-UV MCD spectra show an unusually high-energy Fe(II) → αKG π* metal-to-ligand charge transfer transition in (Fe(II)/αKG)FIH which is red-shifted upon CAD binding. This red shift indicates formation of H-bonds to the αKG that lower the energy of its carbonyl LUMO, activating it for nucleophilic attack by the Fe-O2 intermediate formed along the reaction coordinate.

Comparative genomic analysis of four representative plant growth-promoting rhizobacteria in Pseudomonas

Background

Some Pseudomonas strains function as predominant plant growth-promoting rhizobacteria (PGPR). Within this group, Pseudomonas chlororaphis and Pseudomonas fluorescens are non-pathogenic biocontrol agents, and some Pseudomonas aeruginosa and Pseudomonas stutzeri strains are PGPR. P. chlororaphis GP72 is a plant growth-promoting rhizobacterium with a fully sequenced genome. We conducted a genomic analysis comparing GP72 with three other pseudomonad PGPR: P. fluorescens Pf-5, P. aeruginosa M18, and the nitrogen-fixing strain P. stutzeri A1501. Our aim was to identify the similarities and differences among these strains using a comparative genomic approach to clarify the mechanisms of plant growth-promoting activity.

Results

The genome sizes of GP72, Pf-5, M18, and A1501 ranged from 4.6 to 7.1 M, and the number of protein-coding genes varied among the four species. Clusters of Orthologous Groups (COGs) analysis assigned functions to predicted proteins. The COGs distributions were similar among the four species. However, the percentage of genes encoding transposases and their inactivated derivatives (COG L) was 1.33% of the total genes with COGs classifications in A1501, 0.21% in GP72, 0.02% in Pf-5, and 0.11% in M18. A phylogenetic analysis indicated that GP72 and Pf-5 were the most closely related strains, consistent with the genome alignment results. Comparisons of predicted coding sequences (CDSs) between GP72 and Pf-5 revealed 3544 conserved genes. There were fewer conserved genes when GP72 CDSs were compared with those of A1501 and M18. Comparisons among the four Pseudomonas species revealed 603 conserved genes in GP72, illustrating common plant growth-promoting traits shared among these PGPR. Conserved genes were related to catabolism, transport of plant-derived compounds, stress resistance, and rhizosphere colonization. Some strain-specific CDSs were related to different kinds of biocontrol activities or plant growth promotion. The GP72 genome contained the cus operon (related to heavy metal resistance) and a gene cluster involved in type IV pilus biosynthesis, which confers adhesion ability.

Conclusions

Comparative genomic analysis of four representative PGPR revealed some conserved regions, indicating common characteristics (metabolism of plant-derived compounds, heavy metal resistance, and rhizosphere colonization) among these pseudomonad PGPR. Genomic regions specific to each strain provide clues to its lifestyle, ecological adaptation, and physiological role in the rhizosphere.